joint_territories: Jointly measured spatial omic assays territories

In patrickCNMartin/Vesalius: Vesalius: Dissecting Tissue Anatomy from Spatial Transcriptomic Data

Jointly measured spatial omic assays territories

Description

Jointly measured spatial omic assays territories

Usage

joint_territories(
  mod1,
  mod2,
  dimensions = seq(1, 30),
  embedding = "last",
  method = "interlace",
  norm_method = "log_norm",
  dim_reduction = "PCA",
  signal = "variable_features",
  verbose = TRUE
)

Arguments

mod1	vesalius_assay object containing first modality
mod2	vesalius_assay objecty containing second modality
dimensions	numeric vector describing latent space dimensions to use during intergration
method	character - integration method. interlace - mean - concat are available options
norm_method	character - which count values should be use for integration when using concat method
dim_reduction	characater - which dim reduction methods should be used for concat integration (PCA,PCA_L,UMAP,LSI,LSI_UMAP,NMF)
verbose	logical - should progress message be outputed to the console.

Value

vesalius object containing new image embeddings

patrickCNMartin/Vesalius documentation built on April 17, 2025, 11:31 p.m.